R: Fragment dataset of 13 time-point mouse microarray time...
DellaGattaData
R Documentation
Fragment dataset of 13 time-point mouse microarray time series of gene expression ratios and
and a ranking list of TP63 targets suggested by TSNI.
Description
exprs_tp63_RMA
100 gene reporters of 13 time-points mouse Affymetrix
microarray gene expression coming from a study on primary mouse keratinocytes
with an induced activation of the TRP63 transcription factor (GEO-accession
number:GSE10562, see Source section), where a reverse-engineering algorithm was developed
(TSNI: time-series network identification) to infer the direct targets of TRP63
(Della Gatta et.al. 2008). The data has been processed using rma
(affy) and the profiles are centred (zero-mean) across the timepoints.
DGatta_labels_byTSNI, DGatta_labels_byTSNItop100
a ranking list suggested based by
TSNI is provided. The inferred direct targets were biologically confirmed by
correlation with ChIP-Seq binding regions; therefore the list is used as a
noisy ground truth. See Source section.
genesymbols
Names of the genes that the transcipt_IDs (in exprs_tp63_RMA) correspond to.
gpregeOutput
Its field 'rankingScores' contains log-marginal likelihood ratios,
used as ranking scores, for each gene reporter in exprs_tp63_RMA.
This is the output from a run of gprege on the full DellaGatta dataset
(see demTp63Gp1.R) and stored here for convenience.
Della Gatta G, et al.
Direct targets of the TRP63 transcription factor revealed by a combination of
gene expression profiling and reverse engineering.
Genome Research 2008, 18(6):939.